For a time, the mosque was the largest in the world; its minaret, the Malwiya Tower, is a spiralling cone 52 metres (171 ft) high and 33 metres (108 ft) wide with a spiral ramp. The reign of Al-Mutawakkil had a great effect on the appearance of the city, for he seemed to have been a lover of architecture, and the one responsible for building the great Mosque of Samarra. Al-Mutawakkil and his hired workers as well as other people from the area constructed this mosque using baked brick octagon piers that included four marble columns in the corners. The marble columns were imported, which draws on the fact that Al-Mutawakkil hired artists and architects from all over the Abbasid empire to help him construct the Great Mosque. In a list of his building projects which appears in several different versions, the new Congregational Mosque and up to twenty palaces are mentioned, totalling between 258 and 294 million dirhams. The new Congregational Mosque, with its spiral minaret, built between 849 (235 AH) and 851 (235 AH), formed part of an extension of the city to the east, extending into the old hunting park.

The mind behind the mosque, Al-Mutawakkil, was assassinated in 861, and structures like this mosque were then difficult to credit to a subsequent caliph. There was unrest and a ten year period of trouble, including a civil war in 865–866. This Great Mosque was one of the last buildings with a known name attributed to it in this period.

The mosque itself was destroyed in 1278 C.E. (656 A.H.), after Hulagu Khan’s invasion of Iraq. Only the outer wall and its minaret remain. However, the Iraqi State Organization of Antiquities have been working closely with historians and architects in a restoration process starting in 1956. They tasked people to restore various monuments in Samarra including the Great Mosque. There was extensive restoration done to both the courtyard of the mosque as well as the spiral minaret. Previously only 6 steps remained in the minaret and very few complete arches surrounding the courtyard.